Problem with biomaRt::select
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@analeonpalacio-18199
Last seen 8 months ago
Spain

I am having problems when executing the function select.

ensembl_connection = biomaRt::useEnsembl("snp", dataset = "hsapiens_snp") ensembl_phenotypes = biomaRt::searchFilterValues(mart = ensembl_connection, filter = "phenotype_description", pattern = "migraine") phenotype_expression = paste(ensembl_phenotypes, collapse="|") retrieve_columns = c('refsnp_id', 'chr_name', 'phenotype_description', 'associated_variant_risk_allele', 'allele', 'chrom_start', 'chrom_end', 'associated_gene', 'polyphen_prediction', 'sift_prediction', 'synonym_name') k<-biomaRt::keys(ensembl_connection, keytype="phenotype_description", pattern = phenotype_expression) result <- biomaRt::select(ensembl_connection, keys=k, columns=retrieve_columns, keytype='phenotype_description')

Output

<simpleError in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')">

R session

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C LC_TIME=Spanish_Spain.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.6.3 ulises_0.2.4 tools_3.6.3 bioPROS4Ulises_0.2.9

biomaRt • 224 views
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shepherl 2.8k
@lshep
Last seen 4 hours ago
United States

Please see similar posts. These should be corrected if you update your version of R and use the most recent version of Bioconductor. There were changes in CRAN dplyr package, that have thus been corrected. We do not backport to past releases. If updating R is not an option (althought the recommended action) , you will have to downgrade your version of dplyr.

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Thanks. I had to update R and biomaRt. Everything seems to work fine now

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